Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SOX9

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MCF7ras cells
cell type
human breast cancer cell line
treatment
2 ug/ml doxycycline for three days.
chip antibody
SOX9 (Millipore, AB5535)
geo_loc_name
missing
collection_date
missing

Sequenced DNA Library

library_name
GSM5830719
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% PFA at room temperature for 10 minutes, quenched with 125 mM Glycine, and rinsed twice with 1X PBS. Cells were lysed and sonicated at 4 °C using a Bioruptor Sonicator into 100-600 bp fragments. The samples were incubated overnight at 4 °C with Dynabeads Protein A, which had been pre-coated with 5 µg anti-SOX9 (Millipore, AB5535). The ChIP samples were then washed, eluted, and reverse cross-linked by overnight incubation at 65 °C. Afterward, ChIP-DNA was purified by Phenol:Chloroform:Isoamyl Alcohol and mixed with 5% spike-in mouse gDNA for ChIP-seq. ChIP-Seq library preparation and sequencing reactions were conducted at GENEWIZ, Inc/Azenta US, Inc. (South Plainfield, NJ, USA). NEB NextUltra DNA Library Preparation kit was used following the manufacturer's recommendations. Sequencing was performed using a 2x150 Paired End (PE) configuration on Illumina HiSeq 4000.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
49083498
Reads aligned (%)
67.2
Duplicates removed (%)
11.4
Number of peaks
1090 (qval < 1E-05)

hg19

Number of total reads
49083498
Reads aligned (%)
66.5
Duplicates removed (%)
11.7
Number of peaks
355 (qval < 1E-05)

Base call quality data from DBCLS SRA